Approximating subtree distances between Phylogenies

We give a 5-approximation algorithm to the rooted Subtree-Prune-and-Regraft (rSPR) distance between two phylogenies, which was recently shown to be NP-complete by Bordewich and Semple [5]. This paper presents the first approximation result for this important tree distance. The algorithm follows a standard format for tree distances such as Rodrigues et al. [24] and Hein et al. [13]. The novel ideas are in the analysis. In the analysis, the cost of the algorithm uses a \cascading" scheme that accounts for possible wrong moves. This accounting is missing from previous analysis of tree distance approximation algorithms. Further, we show how all algorithms of this type can be implemented in linear time and give experimental results

Approximating Subtree Distances Between Phylogenies

We give a 5-approximation algorithm to the rooted Subtree-Prune-and-Regraft (rSPR) distance between two phylogenies, which was recently shown to be NP-complete by Bordewich and Semple [5]. This paper presents the first approximation result for this important tree distance. The algorithm follows a standard format for tree distances such as Rodigues et al. [22] and Hein et al. [11]. The novel ideas are in the analysis. In the analysis, the cost of the algorithm uses a “cascading ” scheme that accounts for possible wrong moves. This accounting is missing from previous analysis of tree distance approximation algorithms. Further, we show how all algorithms of this type can be implemented in linear time and give experimental results

IBM’s PIQUANT in TREC2003

For the most part, the system we used for TREC2003 was a smooth evolution of the one we ran in TREC2002 [Chu-Carroll et al, 2003b]. We continued to use our multi-source and multi-agent architecture. For Factoid questions we used all of our previous answering agents with an additional pattern-based agent, an enhanced answer resolution algorithm, and increased coverage of the Cyc sanity checker. We wil

Approximating subtree distances between Phylogenies

We give a 5-approximation algorithm to the rooted Subtree-Prune-and-Regraft (rSPR) distance between two phylogenies, which was recently shown to be NP-complete by Bordewich and Semple [5]. This paper presents the first approximation result for this important tree distance. The algorithm follows a standard format for tree distances such as Rodrigues et al. [24] and Hein et al. [13]. The novel ideas are in the analysis. In the analysis, the cost of the algorithm uses a \cascading" scheme that accounts for possible wrong moves. This accounting is missing from previous analysis of tree distance approximation algorithms. Further, we show how all algorithms of this type can be implemented in linear time and give experimental results